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  • Imputing missing data in aligned sequences

    - by Kwame Oduro
    I want a simple perl script that can help me impute missing nucleotides in aligned sequences: As an example, my old_file contains the following aligned sequences: seq1 ATGTC seq2 ATGTC seq3 ATNNC seq4 NNGTN seq5 CTCTN So I now want to infer all Ns in the file and get a new file with all the Ns inferred based on the majority nucleotide at a particular position. My new_file should look like this: seq1 ATGTC seq2 ATGTC seq3 ATGTC seq4 ATGTC seq5 CTCTC A script with usage: "impute_missing_data.pl old_file new_file" or any other approach will be helpful to me. Thank you.

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  • C++ game designing & polymorphism question

    - by Kotti
    Hi! I'm trying to implement some sort of 'just-for-me' game engine and the problem's plot goes the following way: Suppose I have some abstract interface for a renderable entity, e.g. IRenderable. And it's declared the following way: interface IRenderable { // (...) // Suppose that Backend is some abstract backend used // for rendering, and it's implementation is not important virtual void Render(Backend& backend) = 0; }; What I'm doing right now is something like declaring different classes like class Ball : public IRenderable { virtual void Render(Backend& backend) { // Rendering implementation, that is specific for // the Ball object // (...) } }; And then everything looks fine. I can easily do something like std::vector<IRenderable*> items, push some items like new Ball() in this vector and then make a call similiar to foreach (IRenderable* in items) { item->Render(backend); } Ok, I guess it is the 'polymorphic' way, but what if I want to have different types of objects in my game and an ability to manipulate their state, where every object can be manipulated via it's own interface? I could do something like struct GameState { Ball ball; Bonus bonus; // (...) }; and then easily change objects state via their own methods, like ball.Move(...) or bonus.Activate(...), where Move(...) is specific for only Ball and Activate(...) - for only Bonus instances. But in this case I lose the opportunity to write foreach IRenderable* simply because I store these balls and bonuses as instances of their derived, not base classes. And in this case the rendering procedure turns into a mess like ball.Render(backend); bonus.Render(backend); // (...) and it is bad because we actually lose our polymorphism this way (no actual need for making Render function virtual, etc. The other approach means invoking downcasting via dynamic_cast or something with typeid to determine the type of object you want to manipulate and this looks even worse to me and this also breaks this 'polymorphic' idea. So, my question is - is there some kind of (probably) alternative approach to what I want to do or can my current pattern be somehow modified so that I would actually store IRenderable* for my game objects (so that I can invoke virtual Render method on each of them) while preserving the ability to easily change the state of these objects? Maybe I'm doing something absolutely wrong from the beginning, if so, please point it out :) Thanks in advance!

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  • Django: What's the correct way to get the requesting IP address?

    - by swisstony
    I'm trying to develop an app using Django 1.1 on Webfaction. I'd like to get the IP address of the incoming request, but when I use request.META['REMOTE_ADDR'] it returns 127.0.0.1. There seems to be a number of different ways of getting the address, such as using HTTP_X_FORWARDED_FOR or plugging in some middleware called SetRemoteAddrFromForwardedFor. Just wondering what the best approach was?

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  • Grails query not using GORM

    - by Tihom
    What is the best way to query for something without using GORM in grails? I have query that doesn't seem to fit in the GORM model, the query has a subquery and a computed field. I posted on stackoverflow already with no response so I decided to take a different approach. I want to query for something not using GORM within a grails application. Is there an easy way to get the connection and go through the result set?

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  • Can I assigin value dynamically like this?

    - by kumar
    <input type="text" id="Date-<%=Model.ID%>" value= " + <%=Html.DisplayFor(model=>model.Date)%> + " /> is this right? i am trying to display value in input box dynamically? can anyone advice me is this corect approach? but still I am getting here only + + in input box? thanks

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  • Flex Builder AS3 Project migration

    - by Fahim Akhter
    Hi, I am developing a Flash game using as3, I chose flex Builder with an AS3 project. Now I am thinking that if selecting the project to be a flex project instead of as3 project I would have a lot of flex functionality like a swf loader,preloaders and the popup manager etc. The graphic components would obviously have been made in flash and used through the swc (avoiding the heavy mxml components). Need to know what other developers think of this approach.

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  • Wrapping a Delphi TFrame descendant as an ActiveX control

    - by Mmarquee
    I am trying to wrap up a TFrame descendant as an ActiveX control, but don't seem to be able to get the control to show up in the ActiveX Control wizard. Is this approach possible, and if so, are there any working examples that I can be pointed at. I have tried to follow the instructions here, but as I said the control show in the list of available controls. Thanks in advance.

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  • Linux Distro - GUI similar to Windows

    - by DeaconDesperado
    I am in the process of refurbing several older laptop machines for use by a couple college guys we have in training to learn basic web development in python. These are students who intern at my company and are hoping to do some work when the summer comes building simple client-oriented webapps (learning the basics of OOP, MVC webapp design in flask, etc.). We're trying to function as the "practical" side of their education. I would like to get them set up on these machines we have sitting about, but I'd like to use a linux distro that would have a gui that closely approximates what they are being compelled to use at school (windows.) I don't really have much of a preference as far as GUI goes since much of what we'll be learning together is accomplished on the command line. I just see this as an easier adjustment for them while they are still reliant on a graphical environment. In the past I'd go straight for Ubuntu, but since they started using the Unity GUI the responsiveness overall can be pretty clunky on older machines, especially since these machines (there are four of them) run the gambit on specs (though all are at least 1.0Ghz and none have anything better than basic integrated video.) Has anyone had to setup a similar working environment in Mint, bare Debian or Zorin? Thanks.

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  • Download and Archive Web Pages on the iPhone

    - by Stefan
    Hi, how do I download and archive full web pages (HTML, CSS, JS, images) on the iPhone? I know how to download the single files. But is there any existing approach to get all files (e.g. all included javascripts), which are linked with a particular web page?

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  • Asp.net: Implementing Auto-Logout functionality

    - by renegadeMind
    Hi, I have to implement auto-logout functionality in one of my projects and i just cant figure out where to start looking for ideas but SO. What i need is for the application to redirect the user to the login page if the user session has expired. Please tell me as to what should be my approach to tackle this requirement. Problem Statement: If the user leaves the system for more than n minutes in any given log-in instance, the system should automatically log them off.

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  • similar to __asm int 3 in Max OS X/ Xcode?

    - by Mark
    Hi, When using visual studio to develop c++ applications, I used to write _asm int 3; and then build the application. When the application is executed, if the code path that has "_asm int 3" is encountered Visual Studio Debugger used to get lauched and I could debug the problems. Is there any similar approach when developing using Xcode on Mac OS X? Thanks a lot. Mark

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  • What is the best forum plug-in solution for the Symfony framework?

    - by Zoja
    I'm looking for a good solution to integrate a forum into a symfony application. Something like phpBB would be excellent. I've seen phpBB plugins to integrate with symfony but that's not enough for my purposes, also, mapping database tables is a lame approach in my opinion. If anybody knows a good working forum component for Symfony then I would really apreciate it. :) Thanks!

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  • url optimization in rails?

    - by piemesons
    Hello I want to create seo optimize url in rails.Same like done in stackoverflow. Right now this is my url http://localhost:3000/questions/56 I want to make it something like this:- http://localhost:3000/questions/56/this-is-my-optimized-url i am using restful approach. is there any plug-in available for this.

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  • Asp.net deployment with remote desktop

    - by Efe Kaptan
    Hi, i have a production server that does not have ftp access. Possible way to deploy files is connecting with remote desktop client and send files. As you know this approach is highly hard and time inefficient. Could you please provide me best practices to deploy in a more fast way? Thanks

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  • Checking for duplicates in a vector

    - by xbonez
    I have to check a vector for duplicates. What is the best way to approach this: I take the first element, compare it against all other elements in the vector. Then take the next element and do the same and so on. Is this the best way to do it, or is there a more efficient way to check for dups?

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  • Backbone: Easiest way to maintain reference to 'this' for a Model inside callbacks

    - by Garrett
    var JavascriptHelper = Backbone.Model.extend("JavascriptHelper", {}, // never initialized as an instance { myFn: function() { $('.selector').live('click', function() { this.anotherFn(); // FAIL! }); }, anotherFn: function() { alert('This is never called from myFn()'); } } ); The usual _.bindAll(this, ...) approach won't work here because I am never initializing this model as an instance. Any ideas? Thanks.

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  • Best solution for a windows service with constant running threads in C# 4.0

    - by dagda1
    Hi, I want to create a windows service that will create x number of threads that wake up every x number of minutes and do some work. I think the task scheduling or parallel framework is a bad fit for this type of work as it is best suited for work that starts, completes and finishes rather than is constant. Should I look at utilising a thread pool for this approach or does anyone have any advice for a good solution? Thanks Paul

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